-Unlike other aspect seeking missiles in the game, the Hornet is unusual in that it does not lead the target, instead it follows a pure/lag pursuit curve. This means it has trouble hitting moving targets if it approches them head on, they are best fired from within a 60degree cone of the target's rear. A lot of people don't notice this and have a hard time hitting anything with the Hornet as a result.
-The game doesn't really explain very well the fact that some ships may have more than one mount for their primary weapon slots. For example, the second primary slot on the Myrmidon fighter actually mounts 4 guns instead of 2 while the first slot only mounts 2.
-Likewise missile banks don't all have the same capacity. For example, the 3rd missile bank on the Myrmidon is much larger than the first 2, making it better for mounting dumbfire missiles like the Tempest.
-Remember, the crosshair only shows where the ship is pointing, not necessarily where your guns are pointing. Unlike some other games, the projectiles in Freespace 2 do not converge at a point in front of the ship, they shoot straight forward from where where the guns are mounted, so the way the guns are positioned on a particular ship does matter. Again, the Myrmidon is a good example because all of its guns are actually mounted higher than the cockpit, so you might have to aim slightly lower to hit your target. This becomes even more apparent on ships like the Ursa where the gun mounts are asymmetrical.
-Many players don't notice the fact that turning left and right does not make the ship do a perfect rotation around that axis, you actually roll slowly in the direction you are turning. This is actually quite clever in that it allows you to make some smoother turns by pitching up afterwards, but players expecting a nice flat turn sometimes get thrown off by this. If you want a flat curve you have to roll the ship on its side and pitch up or down. (if you ever wondered why your enemies tend to end up above the screen when you turn left or right to face them, now you know.)
-The support ship. It's not so much an obscure feature, but it's something that a lot of players forget to use and make things harder on themselves as a result.
-There is a neat little feature called target padlock camera that isn't enabled by default, you have to go into options and assign a key to it (it's under misc. controls). What it does is it frees the Main Flight Controller (the oval shape group of HUD elements in the middle of the screen around the crosshair) and turns the camera to keep sight of your current target. Your ship will continue to fly in the direction indicated by the crosshair, but now the camera is now locked on your current target. If you turn the ship so that the crosshair and MFC are no longer on screen there will be an arrow on the edge of the screen to indicate where it is. It's a bit awkward to use at first, but some players find it useful for keeping sight of their targets in close dogfights.
-There is also a 3rd person behind the ship view that can be toggled on and off if you prefer to play that way.
-Contrary to popular belief, Freespace 2 does support lateral thrusters and gliding, but they're not mounted on most of the ships the player gets to use so normally the player does not get to use them (presumably this is for game balance reasons). However, a few Shivan ships do have lateral thrusters and they do use them in combat. There is one mission Special Operations Command mission in the campaign where you get to fly a captured Mara where you can use lateral thrusters, but they aren't bound to any keys by default.
-There is time acceleration in the game that can be assigned to couple keys. Personally I don't think there are any quiet bits in the missions long enough to really make time acceleration necessary, but if you want to use it you can assign the keys in the options menu.